# Estimation of Bayesian model of a bone section Estimation of Bayesian model of a bone section./r Get information using ?MHalgoGen. ```r BP_FitBayesianCompactness( bone = stop("A result from BP_FitMLCompactness() must be provided"), priors = NULL, n.iter = 10000, n.chains = 1, n.adapt = 5000, thin = 10, analysis = 1, adaptive = TRUE, silent = TRUE ) ``` ## Arguments - `bone`: The bone image to be used - `priors`: Priors - `n.iter`: Number of iterations - `n.chains`: Number of chains - `n.adapt`: Number of iteration to adapt - `thin`: Thin parameter for analysis - `analysis`: Name or rank of analysis - `adaptive`: Should SDProp be changed during iterations - `silent`: Should some information must me shown ? ## Returns The -Ln L ## Details BP_FitBayesianCompactness estimates Bayesian model of a bone section ## Examples ```r ## Not run: # Not run: library(BoneProfileR) path_Hedgehog <- system.file("extdata", "Erinaceus_europaeus_fem_2-1_small.png", package = "BoneProfileR") bone <- BP_OpenImage(file=path_Hedgehog) bone <- BP_DetectBackground(bone=bone, analysis="logistic") bone <- BP_DetectForeground(bone=bone, analysis="logistic") bone <- BP_DetectCenters(bone=bone, analysis="logistic") bone <- BP_EstimateCompactness(bone, analysis="logistic") bone <- BP_FitMLCompactness(bone, analysis="logistic") plot(bone) plot(bone, type="observations") plot(bone, type="observations+model", analysis=1) fittedpar <- BP_GetFittedParameters(bone, analysis="logistic", ML=TRUE, return.all=FALSE)[, "mean"] bone <- BP_DuplicateAnalysis(bone, from="logistic", to="flexit") bone <- BP_FitMLCompactness(bone, fitted.parameters=c(fittedpar, K1=1, K2=1), fixed.parameters=NULL, analysis="flexit") compare_AIC(Logistic=BP_GetFittedParameters(bone, analysis="logistic", ML=TRUE, return.all=TRUE), Flexit=BP_GetFittedParameters(bone, analysis="flexit", ML=TRUE, return.all=TRUE)) out4p <- plot(bone, type="observations+model", analysis="logistic") out6p <- plot(bone, type="observations+model", analysis="flexit") bone <- BP_FitBayesianCompactness(bone, analysis="logistic") plot(bone, type="observations+model", CI="MCMC", analysis="logistic") bone <- BP_FitBayesianCompactness(bone, analysis="flexit") plot(bone, type="observations+model", CI="MCMC", analysis="flexit") ## End(Not run) ``` ## See Also Other BoneProfileR: `BP_AutoFit()`, `BP_ChooseBackground()`, `BP_ChooseCenter()`, `BP_ChooseForeground()`, `BP_DetectBackground()`, `BP_DetectCenters()`, `BP_DetectForeground()`, `BP_DuplicateAnalysis()`, `BP_EstimateCompactness()`, `BP_FitBayesianPeriodicCompactness()`, `BP_FitMLCompactness()`, `BP_FitMLPeriodicCompactness()`, `BP_FitMLRadialCompactness()`, `BP_GetFittedParameters()`, `BP_ListAnalyses()`, `BP_LnLCompactness()`, `BP_OpenImage()`, `BP_Report()`, `Erinaceus_europaeus`, `plot.BoneProfileR()`, `summary.BoneProfileR()` ## Author(s) Marc Girondot marc.girondot@gmail.com

BP_FitBayesianCompactness function